Well presumably Trump would pardon Gates too. But he flipped. Same with Flynn. But Flynn did so to protect his son. NBC reported that Trump was telling friends he was confident Manafort would not flip. And the only reason he'd say that is because Manafort could incriminate him. The issue is, Gates is likely knowledgeable of Manafort wrong-doing. And could be a witness in any Manafort/Trump wrong-doings.
Since Manafort is obviously a serious target of Mueller, Gates flipping is bad for him. If Manafort feels Trump will pardon him no matter what, so be it. But imagine the push back should Manafort be indicted for some very serious treason-ish behavior and Trump pardons him... So if you're Manafort you have to really be comfortable in that pardon. If Mueller gets enough on Manafort that he wont take his chances with a pardon, then he flips. If Mueller gets leverage on anyone Manafort would protect, such as a family member (which has been rumored), he flips.
And there is also a New York investigation going on. If Trump or his allies get indicted on state charges, there is no pardon option (Trump can only pardon federal crimes).